RESUMO
Group A rotavirus (RVA) sequences were detected in 10.8% (23/212) and 20.7% (87/421) of fecal samples collected in 2017-2022 from wild boars and domestic pigs, using next-generation sequencing. Complete genome sequence analysis of one wild boar and 13 domestic pig RVAs revealed that six of them carried the rare H2 NSP5 genotype. Out of the 39 samples for which the NSP5 genotype could be determined, 23 (59.0%) were of genotype H2. H2 porcine RVAs consist exclusively of Japanese porcine RVAs and exhibit sequence diversity in each segment, suggesting that H2 porcine RVAs may have evolved through reassortment within the Japanese pig population.
Assuntos
Rotavirus , Sus scrofa , Suínos , Animais , Rotavirus/genética , Japão/epidemiologia , Prevalência , Genômica , GenótipoRESUMO
Rotavirus C (RVC) is a major cause of diarrhoea in swine, cattle, and humans worldwide. RVC exhibits sequence diversity in all 11 genes, especially in VP4 and VP7, and all segment-based genotyping has been performed similar to rotavirus A. To date, recombination events have been reported in rotavirus A and B. However, there are no reports describing gene recombination of RVC, except for recombination in NSP3 between RVC and rotavirus H. In this study, nine porcine RVC strains identified in Japanese pigs were completely sequenced and analysed together with RVC sequences from the GenBank database. The analyses showed that sequences of the VP4, VP2, and NSP1 of several porcine RVC strains did not branch with any of those of the RVC strains in the GenBank database, suggesting new genotypes. Several homologous recombination events, between or within genotypes, were identified in the VP4, VP7, VP2, NSP1, and NSP3 genes. Of these, nine, one, and one intergenotypic recombination events in the VP4, VP2, and NSP3 genes, respectively, were supported with sufficient statistical values. Although these findings suggest occurrences of the intragenic recombination events in the RVC genome, potential sequence errors and poor sequence assemblies in the databases should be watched with care. The results in this study present data about the important recombination events of the RVCs, which influence evolution of the virus by aiding them to gain genetic diversity and plasticity, although further sequence data will be necessary to obtain more comprehensive understanding of such mechanisms.
Assuntos
Infecções por Rotavirus , Rotavirus/genética , Doenças dos Suínos/virologia , Animais , Bovinos , Variação Genética , Genoma Viral , Humanos , Infecções por Rotavirus/veterinária , Infecções por Rotavirus/virologia , SuínosRESUMO
Mammalian orthoreoviruses (MRVs) are non-enveloped double-stranded RNA viruses with a broad host range. MRVs are prevalent worldwide, and in Japan, they have been isolated from various hosts, including humans, dogs, cats, wild boars, and pigs, and they have also been found in sewage. However, Japanese porcine MRVs have not been genetically characterized. While investigating porcine enteric viruses including MRV, five MRVs were isolated from the feces of Japanese pigs using MA104 cell culture. Genetic analysis of the S1 gene revealed that the Japanese porcine MRV isolates could be classified as MRV-2 and MRV-3. Whole genome analysis showed that Japanese porcine MRVs exhibited genetic diversity, although they shared sequence similarity with porcine MRV sequences in the DDBJ/EMBL/GenBank database. Several potential intragenetic reassortment events were detected among MRV strains from pigs, sewage, and humans in Japan, suggesting zoonotic transmission. Furthermore, homologous recombination events were identified in the M1 and S1 genes of Japanese porcine MRV. These findings imply that different strains of Japanese porcine MRV share a porcine MRV genomic backbone and have evolved through intragenetic reassortment and homologous recombination events.
Assuntos
Orthoreovirus de Mamíferos , Humanos , Suínos , Animais , Cães , Orthoreovirus de Mamíferos/genética , Filogenia , Fezes , Especificidade de Hospedeiro , Variação Genética , MamíferosRESUMO
Posaviruses and posa-like viruses are unclassified viruses with sequence similarity to viruses of the order Picornavirales. They have been reported in various vertebrates and invertebrates. We identified 11 posavirus-like sequences in porcine feces and performed phylogenic analysis. Previously reported Japanese posaviruses and those identified in this study clustered with posavirus 1, 4, and 7 and husavirus 1, while five viruses branched into three independent lineages, tentatively named posavirus 10, 11, and 12. Interestingly, posaviruses, except for posavirus 8 and 9, husaviruses, and rasaviruses, formed a cluster consisting of viruses only from pigs, humans, and rats, while posavirus 8 and 9, fisavirus, and basaviruses clustered with posa-like viruses from invertebrates.
Assuntos
Fezes/virologia , Invertebrados/virologia , Vertebrados/virologia , Vírus/classificação , Vírus/genética , Animais , Análise por Conglomerados , Genoma Viral/genética , Humanos , Japão , Metagenômica/métodos , Filogenia , Vírus de RNA/genética , Ratos , Análise de Sequência de DNA/métodos , SuínosRESUMO
The Porcine Sapelovirus (PSV) is an enteric virus of pigs that can cause various disorders. However, there are few reports that describe the molecular characteristics of the PSV genome. In this study, almost the entire genomes of 23 PSVs detected in Japanese pigs were analyzed using bioinformatics. Analysis of the cis-active RNA elements showed that the predicted secondary structures of the internal ribosome entry site in the 5' untranslated region (UTR) and a cis-replication element in the 2C coding region were conserved among PSVs. In contrast, those at the 3' UTR were different for different PSVs; however, tertiary structures between domains were conserved across all PSVs. Phylogenetic analysis of nucleotide sequences of the complete VP1 region showed that PSVs exhibited sequence diversity; however, they could not be grouped into genotypes due to the low bootstrap support of clusters. The insertion and/or deletion patterns in the C-terminal VP1 region were not related to the topology of the VP1 tree. The 3CD phylogenetic tree was topologically different from the VP1 tree, and PSVs from the same country were clustered independently. Recombination analysis revealed that recombination events were found upstream of the P2 region and some recombination breakpoints involved insertions and/or deletions in the C-terminal VP1 region. These findings demonstrate that PSVs show genetic diversity and frequent recombination events, particularly in the region upstream of the P2 region; however, PSVs could currently not be classified into genotypes and conserved genetic structural features of the cis-active RNA elements are observed across all PSVs.
Assuntos
Diarreia/genética , Genoma Viral/genética , Infecções por Picornaviridae/virologia , Picornaviridae/genética , Animais , Diarreia/veterinária , Diarreia/virologia , Fezes/virologia , Variação Genética , Filogenia , Picornaviridae/patogenicidade , Infecções por Picornaviridae/genética , Infecções por Picornaviridae/veterinária , Suínos/genética , Suínos/virologia , Doenças dos Suínos/genética , Doenças dos Suínos/virologiaRESUMO
Porcine kobuviruses (PoKoVs) are ubiquitously distributed in pig populations worldwide and are thought to be enteric viruses in swine. Although PoKoVs have been detected in pigs in Japan, no complete genome data for Japanese PoKoVs are available. In the present study, 24 nearly complete or complete sequences of the PoKoV genome obtained from 10 diarrheic feces and 14 non-diarrheic feces of Japanese pigs were analyzed using a metagenomics approach. Japanese PoKoVs shared 85.2-100% identity with the complete coding nucleotide (nt) sequences and the closest relationship of 85.1-98.3% with PoKoVs from other countries. Twenty of 24 Japanese PoKoVs carried a deletion of 90 nt in the 2B coding region. Phylogenetic tree analyses revealed that PoKoVs were not grouped according to their geographical region of origin and the phylogenetic trees of the L, P1, P2, and P3 genetic regions showed topologies different from each other. Similarity plot analysis using strains from a single farm revealed partially different similarity patterns among strains from identical farm origins, suggesting that recombination events had occurred. These results indicate that various PoKoV strains are prevalent and not restricted geographically on pig farms worldwide and the coexistence of multiple strains leads to recombination events of PoKoVs and contributes to the genetic diversity and evolution of PoKoVs.
Assuntos
Diarreia/veterinária , Fezes/virologia , Genoma Viral , Kobuvirus/genética , Kobuvirus/isolamento & purificação , Infecções por Picornaviridae/veterinária , Doenças dos Suínos/virologia , Animais , Diarreia/virologia , Variação Genética , Japão , Kobuvirus/classificação , Filogenia , Infecções por Picornaviridae/virologia , SuínosRESUMO
During an investigation of porcine fecal viruses using a metagenomics approach, a novel picornavirus was identified from the feces of a healthy two-month-old pig. This virus, named porcine picornavirus Japan (PPVJ), had a standard picornavirus genome organization, including the L protein region. The 5' untranslated region harbored a type II internal ribosomal entry site. This virus was most closely related to lesavirus 1 (amino acid sequence identity: 38.2 %) in P1, equine rhinitis A virus (25.8 %) in P2, and lesavirus 2 (40.9 %) in P3. According to the genus demarcations for the family Picornaviridae (less than 40 %, 40 %, and 50 % amino acid sequence identity in P1, P2, and P3, respectively), PPVJ represents a new genus in the family Picornaviridae. PPVJ was detected in 23.3 % of the fecal samples (from 58.3 % of the farms across a wide area) from pigs less than four months old, by reverse transcription PCR, using specific primers designed from the 3D sequence, followed by sequencing. The host range and pathogenic potential of this virus in animals is yet to be determined.
Assuntos
Picornaviridae/genética , Sus scrofa/virologia , Regiões 5' não Traduzidas , Animais , Fezes/virologia , Genoma Viral , Japão , Conformação de Ácido Nucleico , Filogenia , Picornaviridae/classificação , Picornaviridae/isolamento & purificação , RNA Viral/química , RNA Viral/genética , Reação em Cadeia da Polimerase Via Transcriptase ReversaRESUMO
Recently, there have been reports of new members of posavirus-like viruses in the order Picornavirales. In this study, using a metagenomics approach, 11 posavirus-like sequences (>7,000 nucleotides) were detected in 155 porcine fecal samples. Phylogenetic analysis revealed that the newly identified virus sequences, together with other posavirus-like viruses, form distinct clusters within the order Picornavirales, composed of eight genogroups and unassigned sequences based on amino acid sequences of the helicase and RNA-dependent RNA polymerase regions, with <40 % and <50 % sequence identity, respectively. We propose further classifications of highly diverse posavirus populations based on newly identified sequences from Japanese pig feces.
Assuntos
Fezes/virologia , Variação Genética , Vírus de RNA/classificação , Vírus de RNA/genética , Suínos/virologia , Animais , Análise por Conglomerados , Metagenômica , Filogenia , RNA Helicases/genética , Vírus de RNA/isolamento & purificação , RNA Polimerase Dependente de RNA/genética , Análise de Sequência de DNA , Homologia de SequênciaRESUMO
Porcine diarrhea caused by viruses is a major problem of the pig farming industry and can result in substantial losses of revenue. Thus, diagnosing the infectious agents is important to prevent and control diseases in pigs. We developed novel one-step real-time quantitative RT-PCR (qPCR) assays that can detect four porcine diarrheal viruses simultaneously: porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine deltacoronavirus (PDCoV), and porcine group A rotavirus (PRVA). The qPCR analysis takes only 75 minutes to detect the presence of the four viruses. The limits of detection of our new assays for PEDV, TGEV, PDCoV, and PRVA were 100, 10, 10 and 10 copies per reaction, respectively. The sensitivity of qPCR was 1-1000 times higher than that of published gel-based RT-PCR. We used our qPCR method to successfully diagnose clinical samples from infected pigs, and no false positive results were obtained. In conclusion, qPCR can drastically reduce the diagnostic time to detect viruses compared to currently employed methods. We predict that the qPCR assays will become a useful tool for detecting viral infections that cause diarrhea and other complications in pigs.
Assuntos
Diarreia/veterinária , Reação em Cadeia da Polimerase em Tempo Real/veterinária , Reação em Cadeia da Polimerase Via Transcriptase Reversa/veterinária , Doenças dos Suínos/virologia , Viroses/veterinária , Animais , Diarreia/diagnóstico , Diarreia/virologia , Reação em Cadeia da Polimerase em Tempo Real/métodos , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Sensibilidade e Especificidade , Suínos , Doenças dos Suínos/diagnóstico , Viroses/diagnóstico , Viroses/virologiaRESUMO
From October 2013 to date, approximately 1,000 outbreaks of porcine epidemic diarrhoea virus (PEDV) have occurred in Japan. Porcine epidemic diarrhoea with non-lethal effects in piglets was identified in Tottori prefecture in October 2014. Complete genome analysis revealed that the causative pathogen, Tottori2, is a new PEDV variant with a large (582 nt) deletion in the spike gene. Phylogenetic analysis indicated that the Tottori2 PEDV strain might have been derived from the current PEDV strains circulating in domestic pigs. Moreover, the Tottori2 PEDV strain was successfully isolated in Vero cells by serial passage.
Assuntos
Infecções por Coronavirus/veterinária , Vírus da Diarreia Epidêmica Suína/genética , Deleção de Sequência , Glicoproteína da Espícula de Coronavírus/genética , Doenças dos Suínos/virologia , Sequência de Aminoácidos , Animais , Infecções por Coronavirus/virologia , Dados de Sequência Molecular , Filogenia , Vírus da Diarreia Epidêmica Suína/classificação , Vírus da Diarreia Epidêmica Suína/isolamento & purificação , Vírus da Diarreia Epidêmica Suína/metabolismo , Alinhamento de Sequência , Glicoproteína da Espícula de Coronavírus/química , Glicoproteína da Espícula de Coronavírus/metabolismo , Sus scrofa/virologia , SuínosRESUMO
A viral metagenomics approach was used to investigate fecal samples of Japanese calves with and without diarrhea. Of the different viral pathogens detected, read counts gave nearly complete astrovirus-related RNA sequences in 15 of the 146 fecal samples collected in three distinct areas (Hokkaido, Ishikawa, and Kagoshima Prefectures) between 2009 and 2015. Due to the lack of genetic information about bovine astroviruses (BoAstVs) in Japan, these sequences were analyzed in this study. Nine of the 15 Japanese BoAstVs were closely related to Chinese BoAstVs and clustered into a lineage (tentatively named lineage 1) in all phylogenetic trees. Three of 15 strains were phylogenetically separate from lineage 1, showing low sequence identities, and clustered instead with an American strain isolated from cattle with respiratory disease (tentatively named lineage 2). Interestingly, two of 15 strains clustered with lineage 1 in the open reading frame (ORF)1a and ORF1b regions, while they clustered with lineage 2 in the ORF2 region. Remarkably, one of 15 strains exhibited low amino acid sequence similarity to other BoAstVs and was clustered separately with porcine astrovirus type 5 in all trees, and ovine astrovirus in the ORF2 region, suggesting past interspecies transmission.
Assuntos
Infecções por Astroviridae/veterinária , Doenças dos Bovinos/transmissão , Doenças dos Bovinos/virologia , Bovinos/virologia , Genoma Viral , Mamastrovirus/genética , Sequência de Aminoácidos , Animais , Infecções por Astroviridae/transmissão , Infecções por Astroviridae/virologia , Bovinos/classificação , Fezes/virologia , Feminino , Japão , Masculino , Mamastrovirus/classificação , Mamastrovirus/isolamento & purificação , Dados de Sequência Molecular , Fases de Leitura Aberta , FilogeniaRESUMO
Type 1 recombinant enterovirus G (EV-G), which carries the papain-like cysteine protease (PLCP) gene of torovirus between its 2C/3A regions, and type 2 recombinant EV-G, which carries the torovirus PLCP gene with its flanking regions having non-EV-G sequences in place of the viral structural genes, have been detected in pig farms in several countries. In a previous study, we collected 222 fecal samples from 77 pig farms from 2104 to 2016 and detected one type 2 recombinant EV-G genome by metagenomics sequencing. In this study, we reanalyzed the metagenomic data and detected 11 type 2 recombinant EV-G genomes. In addition, we discovered new type 2 recombinant EV-G genomes of the two strains from two pig farms samples in 2018 and 2019. Thus, we identified the genomes of 13 novel type 2 recombinant EV-Gs isolated from several pig farms in Japan. Type 2 recombinant EV-G has previously been detected only in neonatal piglets. The present findings suggest that type 2 recombinant EV-G replicates in weaning piglets and sows. The detection of type 1 recombinant EV-Gs and type 2 recombinant EV-Gs at 3-year and 2-year intervals, respectively, from the same pig farm suggests that the viruses were persistently infecting or circulating in these farms.
Assuntos
Infecções por Enterovirus , Enterovirus Suínos , Doenças dos Suínos , Suínos , Animais , Feminino , Enterovirus Suínos/genética , Fazendas , Infecções por Enterovirus/veterinária , Japão , Recombinação Genética , Genoma Viral , FilogeniaRESUMO
The bovine leukocyte antigen (BoLA) DRB3*009:02 allele is strongly associated with a low/undetectable bovine leukemia virus (BLV) proviral load. Understanding the status of cattle possessing DRB3*009:02 allele is key for BLV control by breeding. We performed a survey of DRB3*009:02-carrying cattle in two prefectures in Japan using a TaqMan assay developed previously. The allele was found in 3.8% (confidence interval (CI): 3.3-4.3) of 6020 Japanese Black female cattle. A prefecture-level difference was found: the allele was observed in 8.6% CI: 7.5-9.9) of 2242 cattle of the birth prefecture B in Kyushu/Okinawa region, and this percentage was significantly higher than those of prefecture C in Kyushu/Okinawa region (1.3% (CI: 0.4-3.4) of 319) and prefecture A in Chugoku region (0.9% (CI: 0.6-1.4) of 2741), respectively. Consideration on the difference in possession of DRB3*009:02 allele is needed to establish the more efficient control strategy of BLV infection in Japanese Black cattle.
Assuntos
Doenças dos Bovinos , Leucose Enzoótica Bovina , Vírus da Leucemia Bovina , Feminino , Bovinos , Animais , Vírus da Leucemia Bovina/genética , Alelos , Japão/epidemiologia , Antígenos de Histocompatibilidade Classe II/genética , Antígenos Virais/genética , Leucócitos , Doenças dos Bovinos/epidemiologia , Doenças dos Bovinos/genéticaRESUMO
Sigma C protein-coding sequences have been used to phylogenetically classify avian reovirus (ARV) strains. However, the relationship between serotype and phylogenetic cluster classification of the five prototype serotype strains of ARV in Japan has not been established. Thus, we used sigma C protein-coding sequences to characterize avian reoviruses (ARVs) isolated from chickens with tendonitis in Japan together with the five prototype serotype strains of ARV in Japan. Phylogenetic analysis of ARVs based on the sigma C protein-coding sequences revealed that the five prototype serotype strains of ARV were each classified into different, independent clusters. Two field isolates (JP/Tottori/2016 and JP/Nagasaki/2017) that were isolated from chickens with arthritis/tenosynovitis were classified into different clusters. JP/Tottori/2016 was classified into cluster VI with the CS-108 strain, and JP/Nagasaki/2017 was classified into cluster I with strain TS-142. Serologically, JP/Tottori/2016 was well-neutralized by antisera against the CS-108 strain, whereas JP/Nagasaki/2017 cross-reacted with antisera against both the CS-108 and TS-142 strains. Embryo lethality test revealed that the two field isolates induced 80% and 67% embryo mortality, respectively, whereas the five prototype strains induced 0%-33% embryo mortality. Our findings will contribute to understanding the characteristics of ARV strains in Japan.
Nota de investigaciónAnálisis genético de reovirus aviares aislados de pollos en Japón. Se han utilizado secuencias de proteína Sigma C para clasificar filogenéticamente cepas de reovirus aviar (ARV). Sin embargo, no se ha establecido la relación entre el serotipo y la clasificación de grupos filogenéticos de las cinco cepas prototipo de serotipo de reovirus aviares en Japón. Por lo tanto, se utilizó la secuenciación de la proteína sigma C para caracterizar los reovirus aviares (ARV) aislados de pollos con tendinitis en Japón junto con las cinco cepas prototipos de serotipos de reovirus aviares en Japón. El análisis filogenético de los reovirus extranjeros basado en el gene sigma C reveló que las cinco cepas prototipo de serotipo de reoviruses se clasificaron cada una en grupos diferentes e independientes. Dos aislamientos de campo (JP/Tottori/2016 y JP/Nagasaki/2017) que se aislaron de pollos con artritis/tenosinovitis se clasificaron en diferentes grupos. El aislamiento JP/Tottori/2016 se clasificó en el grupo VI con la cepa CS-108, y el aislamiento JP/Nagasaki/2017 se clasificó en el grupo I con la cepa TS-142. Serológicamente, el aislamiento JP/Tottori/2016 fue completamente neutralizado por antisueros contra la cepa CS-108, mientras que el virus JP/Nagasaki/2017 reaccionó de forma cruzada con antisueros contra las cepas CS-108 y TS-142. Las pruebas de patogenicidad de embriones revelaron que los dos aislados de campo indujeron 80% y 67% de mortalidad embrionaria, respectivamente, mientras que las cinco cepas prototipo indujeron 0% -33% de mortalidad embrionaria. Estos hallazgos contribuirán a comprender las características de las cepas de reovirus aviares en Japón.
Assuntos
Orthoreovirus Aviário , Doenças das Aves Domésticas , Infecções por Reoviridae , Animais , Galinhas , Japão/epidemiologia , Orthoreovirus Aviário/genética , Filogenia , Doenças das Aves Domésticas/epidemiologia , Infecções por Reoviridae/epidemiologia , Infecções por Reoviridae/veterináriaRESUMO
Sapoviruses (SaVs) are enteric viruses belonging to the family Caliciviridae that infect humans and animals, including pigs. To date, SaVs have been classified into 19 genogroups (G) based on complete VP1 sequences; however, complete genome sequences of some SaV Gs are not yet available. In this study, we determined the full genome sequences of four SaVs (two GX and two GXI SaVs) and analyzed them together with those of other SaVs. The complete genome sequences of GX and GXI SaVs, excluding the poly(A) tails, were 7124, 7142, 7170, and 7179 nucleotides, which were shorter than those of other SaVs, except for porcine GVI and GVII viruses. Genetic characterization revealed that GX SaVs and GXI SaVs shared common features with GVI and GVII viruses, such as the first 10 amino acid residues in the ORF1 coding region, a shorter ORF1 than that of the other genogroups, and the predicted secondary structure of the 5' end of the genome and the starting region of non-structural protein/structural protein junction. Phylogenetic analyses showed that GX and GXI SaVs branched with porcine GVI, GVII, and GIX SaVs and formed a clade consisting of only porcine SaVs. These findings suggest that porcine GX and GXI SaVs together with porcine GVI, GVII, and possibly GIX SaVs, evolved from a common ancestor in the porcine population.
Assuntos
Sapovirus/genética , Suínos/virologia , Animais , Sequência de Bases , Fezes/virologia , Genoma Viral , Genótipo , Conformação de Ácido Nucleico , Filogenia , RNA Viral/genética , Sapovirus/classificaçãoRESUMO
Enterovirus G (EV-G) belongs to the family of Picornaviridae. Two types of recombinant porcine EV-Gs carrying papain-like cysteine protease (PLCP) gene of porcine torovirus, a virus in Coronaviridae, are reported. Type 1 recombinant EV-Gs are detected in pig feces in Japan, USA, and Belgium and carry the PLPC gene at the junction site of 2C/3A genes, while PLPC gene replaces the viral structural genes in type 2 recombinant EV-G detected in pig feces in a Chinese farm. We identified a novel type 2 recombinant EV-G carrying the PLCP gene with flanking sequences in place of the viral structural genes in pig feces in Japan. The ~0.3â¯kb-long upstream flanking sequence had no sequence homology with any proteins deposited in GenBank, while the downstream ~0.9â¯kb-long flanking sequence included a domain having high amino acid sequence homology with a baculoviral inhibitor of apoptosis repeat superfamily. The pig feces, where the novel type 2 recombinant EV-G was detected, also carried type 1 recombinant EV-G. The amount of type 1 and type 2 recombinant EV-G genomes was almost same in the pig feces. Although the phylogenetic analysis suggested that these two recombinant EV-Gs have independently evolved, type 1 recombinant EV-G might have served as a helper virus by providing viral structural proteins for dissemination of the type 2 recombinant EV-G.
Assuntos
Proteínas Reguladoras de Apoptose/metabolismo , Cisteína Proteases/genética , Infecções por Enterovirus/veterinária , Enterovirus Suínos/genética , Proteínas Estruturais Virais/genética , Animais , Proteínas Reguladoras de Apoptose/genética , Cisteína Proteases/metabolismo , Infecções por Enterovirus/epidemiologia , Infecções por Enterovirus/virologia , Fezes/virologia , Regulação Enzimológica da Expressão Gênica , Regulação Viral da Expressão Gênica , Filogenia , Suínos , Doenças dos Suínos/epidemiologia , Doenças dos Suínos/virologiaRESUMO
Porcine Teschoviruses (PTVs) are associated with polioencephalomyelitis and various diseases, including reproductive and gastrointestinal disorders, of pigs and wild boars, and are also detected in the feces of healthy pigs. The genus Teschovirus contains a single species Teschovirus A that currently includes 13 serotypes. In the present study, we identified novel PTVs that are distantly related to Teschovirus A and were found in fecal samples of pigs with or without diarrhea in Japan. Phylogenetic analysis of amino acid (aa) sequences of the complete coding region revealed that these newly identified viruses did not cluster with any strains of PTVs or other strains within the picornavirus supergroup 1, suggesting that the viruses may not belong to Teschovirus A or any genus of the family Picornaviridae. These novel PTVs share a type IV internal ribosomal entry site and conserved characteristic motifs in the coding region, yet exhibit 62.2-79.0%, 86.6-92.8%, 77.1-81.0%, and 84.3-86.7% aa identities to PTV strains in P1, 2C, 3C, and 3D regions, respectively. In contrast, PTV 1-13 strains of the Teschovirus A share 76.5-92.1%, 88.1-99.7%, 93.2-100%, and 95.8-100% aa identities in the P1, 2C, 3C, and 3D, respectively, within the species. These data imply that the newly identified viruses belong to teschoviruses, and may represent a novel species in the genus Teschovirus.
Assuntos
Fezes/virologia , Metagenômica , Infecções por Picornaviridae/veterinária , Doenças dos Suínos/epidemiologia , Doenças dos Suínos/virologia , Teschovirus/genética , Animais , Genoma Viral , Japão/epidemiologia , Metagenômica/métodos , Conformação de Ácido Nucleico , Filogenia , RNA Viral , Suínos , Teschovirus/classificação , Sequenciamento Completo do GenomaRESUMO
A novel virus related to the Enterovirus/Sapelovirus supergroup in the family Picornaviridae was identified in healthy porcine feces in Japan by using a metagenomics approach. The genome of the virus, named Sapelo-like porcine picornavirus Japan (SPPVJ) Pig/Isi-Im1/JPN/2016, had a type-IV internal ribosomal entry site and carried a 6978-nucleotide-long single open reading frame encoding a 2326 amino acids (aa) polyprotein precursor. The coding sequence region consisted of leader protein (68 aa), a structural protein region P1 (824 aa), and the non-structural protein regions P2 (672 aa) and P3 (762 aa). Among representative picornaviruses, the P1, 2C, and 3CD regions of SPPVJ had the highest aa identities of 64.4%, 61.9%, and 73.3%, respectively, with the corresponding regions of sapelo-like bat picornavirus BtVs-PicoV/SC2013. Sequencing analysis of the RT-PCR products derived from the 5' untranslated and 3D regions revealed the presence of SPPVJ in 17.8% (19/107) of the feces from healthy and diarrheal pigs in 12 farms in 2015-2016. Further studies are needed to determine the origin and pathogenic potential of SPPJV in pigs and other mammals.
Assuntos
Diarreia/veterinária , Fezes/virologia , Genoma Viral , Infecções por Picornaviridae/veterinária , Picornaviridae/genética , Suínos/virologia , Regiões 3' não Traduzidas , Regiões 5' não Traduzidas , Animais , Diarreia/virologia , Enterovirus , Japão/epidemiologia , Metagenômica , Conformação de Ácido Nucleico , Fases de Leitura Aberta , Filogenia , Picornaviridae/classificação , Picornaviridae/isolamento & purificação , RNA Viral/genética , Análise de Sequência de DNA , Proteínas Virais/genéticaRESUMO
To study the genetic diversity of enterovirus G (EV-G) among Japanese pigs, metagenomics sequencing was performed on fecal samples from pigs with or without diarrhea, collected between 2014 and 2016. Fifty-nine EV-G sequences, which were >5,000 nucleotides long, were obtained. By complete VP1 sequence analysis, Japanese EV-G isolates were classified into G1 (17 strains), G2 (four strains), G3 (22 strains), G4 (two strains), G6 (two strains), G9 (six strains), G10 (five strains), and a new genotype (one strain). Remarkably, 16 G1 and one G2 strain identified in diarrheic (23.5%; four strains) or normal (76.5%; 13 strains) fecal samples possessed a papain-like cysteine protease (PL-CP) sequence, which was recently found in the USA and Belgium in the EV-G genome, at the 2C-3A junction site. This paper presents the first report of the high prevalence of viruses carrying PL-CP in the EV-G population. Furthermore, possible inter- and intragenotype recombination events were found among EV-G strains, including G1-PL-CP strains. Our findings may advance the understanding of the molecular epidemiology and genetic evolution of EV-Gs.